tbuckley/cabot-search huggingface dataset:
Endoscopic ultrasound-guided antegrade stenting for benign biliary disease in an elderly patient with altered anatomy (Roux-en-Y)
Authors: Daniel Luna-Rodriguez, Sandra Maisterra, Albert Garcia-Sumalla, Maria Puigcerver-Mas, Joan B. Gornals
Journal: Endoscopy (2022)

A 91-year-old man with multiple pathologies and a history of subtotal gastrectomy with Roux-en-Y reconstruction for an antral ulcer was admitted with acute cholangitis. A hepatobiliary magnetic resonance imaging (MRI) scan showed multiple choledochal stones causing intra- and extrahepatic bile duct dilatation.
A novel elastic ring for suturing colonic anastomotic fistula by colonoscopy
Authors: Shuai-qing Zhang, Zhou-man Yu, Bai-hui Wang, Xiu-li Zuo, Ai-jun Zhang, Ru-yuan Li
Journal: Endoscopy (2022)

A 76-year-old man presented with abdominal pain and fever on the fourth day after laparoscopic radical resection of rectal cancer. Colonoscopy revealed an 0.8 × 0.8-cm colonic anastomotic fistula 8 cm from the anus.
Tunneling technique using a device delivery system for the treatment of pancreaticopleural fistula due to severe downstream pancreatic duct strictures
Authors: Sho Kitagawa, Narito Murakoshi, Keiya Okamura
Journal: Endoscopy (2022)

A 70-year-old man presented with epigastric discomfort. He had undergone a transarterial coil embolization of a splenic artery pseudoaneurysm 3 months previously. Computed tomography revealed an effusion extending from the pancreatic tail towards the mediastinum, with an accompanying pleural effusion ([Fig. 1]). Endoscopic retrograde pancreatography revealed severe ductal strictures in the pancreatic body ([Fig. 2 a]) and a pancreaticopleural fistula upstream of those strictures ([Fig. 2 b]). We then managed to advance a long-tapered catheter beyond the strictures; however, we were unable to pass a nasopancreatic drainage (NPD) tube through the strictures. Therefore, we next opted to perform a "tunneling technique" using a novel device delivery system (EndoSheather; Piolax Medical Devices, Kanagawa, Japan). The device delivery system consists of an inner catheter that tapers to a tip of 3.9 Fr diameter within an outer sheath (6.2 Fr inner diameter), which enables devices of up to 5.7 Fr diameter to successfully pass through tight strictures. Thus, we advanced the delivery system over a 0.035-inch guidewire to dilate the strictures ([Fig. 2 c]), and after removing the inner catheter, we were now able to easily pass a 5-Fr NPD tube through the outer sheath of the device and past the strictures ([Fig. 2 d], [Video 1]). We removed the tube 3 weeks after the treatment and discharged the patient without any further complication.
Portobiliary fistula on single-operator cholangioscopy
Authors: Adnan Aman Khan, Mujtaba Mohamed, Adnan Elghezewi, David Denning, Ahmed Sherif, Wesam Frandah
Journal: Endoscopy (2022)

Portobiliary fistula formation is an exceedingly rare complication following endoscopic retrograde cholangiopancreatography (ERCP), with a scarcity of cases reported in the scientific literature [1] [2]. Patients may present with ensuing – often fatal – gastrointestinal hemorrhage, with challenges in its diagnosis and management as a result.
Endoscopic full-thickness resection with reconstruction of the rectal wall
Authors: Mihajlo Gjeorgjievski, Avik Sarkar, Haroon Shahid, Amy Tyberg, Michel Kahaleh
Journal: Endoscopy (2022)

Endoscopic submucosal dissection (ESD) achieves high rates of en bloc resection and R0 resection regardless of lesion size and minimizes the risk of recurrence [1].
Endoscopic management of gastrojejunocolic fistula as an unusual complication of endoscopic ultrasound-guided gastroenterostomy
Authors: Alzbeta Hujova, Petr Stirand, Patrik Turza, Julius Spicak, Tomas Hucl
Journal: Endoscopy (2022)

Endoscopic ultrasound-guided gastroenterostomy (EUS-GE) using a lumen-apposing metal stent (LAMS) is a novel endoscopic technique for treating gastric outlet obstruction and represents an alternative to stenting or surgery [1] [2]. EUS-GE is minimally invasive and compares favorably with long-term surgical outcomes [1] [2]. Several studies report a high degree of technical and clinical success, despite a considerable rate of complications [1] [3].
Laser lithotripsy to treat a huge incarcerated esophageal bezoar
Authors: Ruifeng Song, Chao Han, Hongjian Wang, Guangzhao Qi, Feng Xu
Journal: Endoscopy (2022)

A 44-year-old man went to the local hospital with a 3-day history of nausea, vomiting, abdominal pain, and difficulty eating after drinking. Gastrointestinal endoscopy showed a kidney-shaped bezoar obstructing the esophagus at 30 cm from incisors. On esophagography, the esophageal walls were seen to be stretched thin by the large bezoar ([Fig. 1]). Computed tomography scanning showed that the bezoar, which was located in the lower esophagus, was about 30-mm wide, 25 mm in the anteroposterior direction, and 53 mm in length ([Fig. 2 a, b]). Multiplanar reformation showed that the bezoar was close to the major blood vessels and heart ([Fig. 2 c]).
A novel technique of intraductal ultrasonography using a newly designed endoscopic sheath and Y-connector during endoscopic retrograde cholangiography
Authors: Koichiro Mandai, Takato Inoue
Journal: Endoscopy (2022)

Intraductal ultrasonography (IDUS) is a useful diagnostic modality for the detection of biliary stones [1]. However, conventional IDUS cannot provide accurate cross-sectional imaging of the bile duct in patients with pneumobilia. To overcome this limitation, we describe a novel IDUS technique using a newly designed endoscopic sheath and Y-connector to confirm complete biliary stone removal.
Tumor MHC class I expression alters cancer-associated myelopoiesis driven by host NK cells
Authors: Shi Yong Neo, Xu Jing, Le Tong, Dongmei Tong, Juan Gao, Ziqing Chen, Mireia Cruz De Los Santos, Nutsa Burduli, Sabrina De Souza Ferreira, Arnika Kathleen Wagner, Evren Alici, Charlotte Rolny, Yihai Cao, Andreas Lundqvist
Journal: Journal for ImmunoTherapy of Cancer (2022)

Downregulation of MHC class I (MHCI) molecules on tumor cells is recognized as a resistance mechanism of cancer immunotherapy. Given that MHCI molecules are potent regulators of immune responses, we postulated that the expression of MHCI by tumor cells influences systemic immune responses. Accordingly, mice-bearing MHCI-deficient tumor cells showed reduced tumor-associated extramedullary myelopoiesis in the spleen. Depletion of natural killer (NK) cells abrogated these differences, suggesting an integral role of immune-regulatory NK cells during tumor progression. Cytokine-profiling revealed an upregulation of TNF-α by NK cells in tumors and spleen in mice-bearing MHCI expressing tumors, and inhibition of TNF-α enhanced host myelopoiesis in mice receiving adoptive transfer of tumor-experienced NK cells. Our study highlights a critical role of NK cells beyond its identity as a killer lymphocyte and more importantly, the potential host responses to a localized tumor as determined by its MHCI expression.
Taming the Selection of Optimal Substitution Models in Phylogenomics by Site Subsampling and Upsampling
Authors: Sudip Sharma, Sudhir Kumar
Journal: Molecular Biology and Evolution (2022)

The selection of the optimal substitution model of molecular evolution imposes a high computational burden for long sequence alignments in phylogenomics. We discovered that the analysis of multiple tiny subsamples of site patterns from a full sequence alignment recovers the correct optimal substitution model when sites in the subsample are upsampled to match the total number of sites in the full alignment. The computational costs of maximum-likelihood analyses are reduced by orders of magnitude in the subsample-upsample (SU) approach because the upsampled alignment contains only a small fraction of all site patterns. We present an adaptive protocol, ModelTamer, that implements the new SU approach and automatically selects subsamples to estimate optimal models reliably. ModelTamer selects models hundreds to thousands of times faster than the full data analysis while needing megabytes rather than gigabytes of computer memory.
Correction: Exploring the safety, effect on the tumor microenvironment, and efficacy of itacitinib in combination with epacadostat or parsaclisib in advanced solid tumors: a phase I study
Journal: Journal for ImmunoTherapy of Cancer (2022)

The last sentence of the section titled 'Group A (itacitinib plus epacadostat)' has been updated to 'Serious TEAEs considered by the investigator to be related to itacitinib and parsaclisib included aseptic meningitis (one in part 1a group B), one each of cardiomyopathy and pneumonitis in groups B-1 and B-2, and one each of lung infection and streptococcal bacteremia in group B-3, B-4, and B-5 population'.
Epstein-Barr virus gH/gL has multiple sites of vulnerability for virus neutralization and fusion inhibition
Authors: Wei-Hung Chen, JungHyun Kim, Wei Bu, Nathan L. Board, Yaroslav Tsybovsky, Yanmei Wang, Anna Hostal, Sarah F. Andrews, Rebecca A. Gillespie, Misook Choe, Tyler Stephens, Eun Sung Yang, Amarendra Pegu, Caroline E. Peterson, Brian E. Fisher, John R. Mascola, Stefania Pittaluga, Adrian B. McDermott, Masaru Kanekiyo, M. Gordon Joyce, Jeffrey I. Cohen
Journal: Immunity (2022)
Dysregulated lipidome of sebum in patients with atopic dermatitis
Authors: Huibin Yin, Zhuoqiong Qiu, Ronghui Zhu, Shangshang Wang, Chaoying Gu, Xu Yao, Wei Li
Journal: Allergy (2022)

Lipids are the major components of skin barrier, mainly produced by keratinocytes and sebaceous glands. Previous studies on barrier dysfunction of atopic dermatitis (AD) mainly focus on the lipids from keratinocytes, whereas the role of sebaceous gland-derived lipids in AD has long been underrecognized.The sebum secreted on the skin surface of AD patients was measured using the Delfin Sebum Scale. Sebum was collected using Sebutape patches and subjected for liquid chromatography tandem-mass spectrometry (LC-MS/MS) analysis. Multivariate data analysis was applied to explore the relationship among the lipidome, clinical features, and sebaceous gland-related molecules.The amount of sebum secreted from sebaceous glands was decreased in AD patients and was negatively correlated with the barrier function and disease severity. LC-MS/MS revealed the lipidome of sebum, which clustered distinctly between AD patients and healthy individuals. Among the differential lipid subclasses, triglycerides (TG) were exclusively decreased in AD patients and correlated with disease severity. The first principal component scores of AD patients, which represented the main signature of the lipidome, were positively correlated with the SCORAD scores and were significantly different across the patient groups with differential clinical symptoms such as skin dryness and pruritus. Further analysis on the previously published transcriptome data revealed aberrant expression of lipid metabolism-related genes in non-lesional skin of AD patients, which was associated with skin inflammation and barrier dysfunction and mainly derived from inner root sheath keratinocytes and sebaceous gland cells.Atopic dermatitis patients demonstrated a deviated lipidome of sebum and aberrant lipid metabolism in sebaceous glands, indicating a possible role of lipids from sebaceous glands in the pathogenesis of AD.
Endoscopic treatment of a postoperative anastomotic stricture in a patient with refractory Crohn’s disease
Authors: Yan Jia, Xianzong Ma, Yurong Tao, Limin Zhang, Jianqiu Sheng, Bing Wu, Peng Jin
Journal: Endoscopy (2022)

A 17-year-old man with recurrent abdominal pain for 8 years was diagnosed with Crohn's disease (CD) with perforation. After surgery, the patient's abdominal pain persisted despite treatment with azathioprine, adalimumab, and infliximab. Laboratory testing revealed a positive fecal occult blood test, markedly elevated fecal calprotectin (698 µg/g) and slightly elevated plasma C-reactive protein (CRP) level (8.5 mg/L). Colonoscopy showed an anastomotic ulcer and stricture. The patient was treated with an intravenous infusion of cyclophosphamide and oral thalidomide. After 6 months, his abdominal pain had disappeared and the inflammatory markers had returned to normal. Colonoscopy showed the anastomotic ulcer had disappeared but the stricture had worsened. Thalidomide therapy was maintained; however, after another 6 months, the patient again experienced abdominal pain and his inflammatory markers were significantly elevated (CRP 14 mg/L, fecal calprotectin 1376 µg/g). Computed tomographic enterography (CTE) showed the anastomotic stricture and thickened bowel wall without a fistula.
Systematic comparison with autoimmune liver disease identifies specific histological features of immune checkpoint inhibitor-related adverse events
Authors: Alexander Coukos, Julien Vionnet, Michel Obeid, Hasna Bouchaab, Solange Peters, Sofiya Latifyan, Alexandre Wicky, Olivier Michielin, Haithem Chtioui, Darius Moradpour, François Fasquelle, Christine Sempoux, Montserrat Fraga
Journal: Journal for ImmunoTherapy of Cancer (2022)

Background Immune checkpoint inhibitors (ICIs) have become a mainstay of cancer treatment. Their immune-boosting quality has one major drawback, their proclivity to induce a broad array of immune-related adverse events (irAEs) affecting, among others, the liver and sharing some similarities with classic autoimmune liver diseases (AILD).We aimed to compare clinical, laboratory and histological features of patients with liver-related irAEs and AILD. Methods We systematically compared liver irAEs with AILD, namely autoimmune hepatitis (AIH) and primary biliary cholangitis, regarding their clinical, laboratory, and histological features. Results Twenty-seven patients with liver irAEs (ICI group) and 14 patients with AILD were identified. We observed three distinct ICI-induced histological liver injury patterns: hepatitic (52%), cholangitic (19%), and mixed (29%). When comparing the ICI and AILD groups, centrilobular injury as well as granuloma formation were more prevalent in the former (p=0.067 and 0.002, respectively). CD4+/CD8+ T cell ratios were heterogeneous between the two groups, without statistically significant difference but with a trend toward increased CD8+ T cells among hepatitic irAEs as compared with AIH. Pattern of liver function test alteration was predictive for the type of irAEs but did not correlate with histological severity. Conclusions Liver irAEs have broad clinical, laboratory and histological presentations. Histological features of irAEs and AILD are distinct, likely underpinning their different immunological mechanisms.
Multifocal ulcerating stenosing enteritis as a novel manifestation of immunoglobulin G4-related disease
Authors: Alejandro Campos-Murguía, Clara L. Martinez-Garcia, Fredy Chable-Montero, Luis E. Zamora-Nava
Journal: Endoscopy (2022)

Immunoglobulin G4 (IgG4)-related disease (IgG4-RD) is a rare systemic fibroinflammatory disease characterized by the presence of tumefactive lesions with dense infiltration of IgG4-positive plasma cells and sometimes serum elevated IgG4 [1]. Seventy-five percent of patients have two or more organs affected, with frequent involvement of the pancreas and the bile ducts [2]. Small-bowel involvement has rarely been reported, with only a few case reports in the literature [3]. The presence of IgG4-bearing plasma cells is essential for its diagnosis; an additional histological characteristic is eosinophil infiltration [1] [2]. There is uncertainty regarding its clinical presentation, diagnostic criteria, and treatment. Management with glucocorticoids may be an appropriate option, as well as, in some cases, immunosuppressive maintenance treatment [4].
KDM6A Loss Recruits Tumor-Associated Neutrophils and Promotes Neutrophil Extracellular Trap Formation in Pancreatic Cancer
Authors: Jing Yang, Lin Jin, Hong Sun Kim, Feng Tian, Zhujun Yi, Karan Bedi, Mats Ljungman, Marina Pasca di Magliano, Howard Crawford, Jiaqi Shi
Journal: Cancer Research (2022)

Lysine (K)-specific demethylase 6A (KDM6A) is a frequently mutated tumor suppressor gene in pancreatic ductal adenocarcinoma (PDAC). However, the impact of KDM6A loss on the PDAC tumor immune microenvironment is not known. This study used a genetically engineered, pancreas-specific Kdm6a knockout (KO) PDAC mouse model and human PDAC tissue samples to demonstrate that KDM6A loss correlates with increased tumor-associated neutrophils and neutrophil extracellular traps (NET) formation, which are known to contribute to PDAC progression. Genome-wide bromouridine sequencing analysis to evaluate nascent RNA synthesis showed that the expression of many chemotactic cytokines, especially CXC motif chemokine ligand 1 (CXCL1), was upregulated in KDM6A KO PDAC cells. KDM6A-deficient PDAC cells secreted higher levels of CXCL1 protein, which in turn recruited neutrophils. Furthermore, in a syngeneic orthotopic mouse model, treatment with a CXCL1 neutralizing antibody blocked the chemotactic and NET-promoting properties of KDM6A-deficient PDAC cells and suppressed tumor growth, confirming CXCL1 as a key mediator of chemotaxis and PDAC growth driven by KDM6A loss. These findings shed light on how KDM6A regulates the tumor immune microenvironment and PDAC progression and suggests that the CXCL1-CXCR2 axis may be a candidate target in PDAC with KDM6A loss.KDM6A loss in pancreatic cancer cells alters the immune microenvironment by increasing CXCL1 secretion and neutrophil recruitment, providing a rationale for targeting the CXCL1-CXCR2 signaling axis in tumors with low KDM6A.
Oligometastases: Emerging Evidence
Authors: Wei Liu, Houda Bahig, David A. Palma
Journal: Journal of Clinical Oncology (2022)

The hypothesis that ablative therapies (such as surgery or radiation) can be used to cure patients with a limited number of metastases was influential in changing practice. Early assertions of efficacy were based on observational studies, often without control groups, showing better-than-expected outcomes. However, in the past decade, new evidence from randomized trials has emerged, which in some cases have affirmed old hypotheses, but in other cases have raised new questions. In this review, we discuss the challenges in defining oligometastatic disease, summarize the randomized evidence evaluating metastasis-directed therapy in patients with oligometastatic disease, provide context for the difficulty in generating randomized evidence, and examine ongoing phase III studies.
Preemptive purse-string suturing technique-assisted endoscopic papillectomy of ampullary adenoma
Authors: Danqing Liu, Meng-meng Hao, Leida Zhang, Teng-qian Tang, Xia Ou, Zhiqing Yang, Wei-hui Liu
Journal: Endoscopy (2022)

Endoscopic papillectomy has been recommended by the European Society of Gastrointestinal Endoscopy for the treatment of ampullary adenomas without intraductal extension [1]; however, it is a challenging procedure that is associated with serious adverse events [2], such as bleeding, which occurs in 11 %–30 % of cases [3]. Techniques used to manage bleeding and perforation include clip closure, but there is no agreement on a standard method [4]. Inspired by the endoscopic purse-string suturing (EPSS) method used for the closure of large gastrointestinal defects or perforations [5], we present a preliminary case of EPSS to facilitate the efficacy and safety of endoscopic papillectomy ([Video 1]).
Artificial intelligence for detecting and delineating a small flat-type early esophageal squamous cell carcinoma under multimodal imaging
Authors: Xianglei Yuan, Xianhui Zeng, Long He, Liansong Ye, Wei Liu, Yanxing Hu, Bing Hu
Journal: Endoscopy (2022)

Early diagnosis of esophageal squamous cell carcinoma (ESCC) is crucial for improving its prognosis. Effective endoscopic biopsy is key to ensuring no missed diagnoses or misdiagnosis of lesions occur and accurate delineation of the margins of lesions is essential for effective biopsies. Recently, the application of artificial intelligence (AI) in the endoscopic diagnosis of early ESCC has increased; however, most AI systems identified early ESCC with rough square frames [1] [2] [3]. For the purpose of precise lesion segmentation, we have developed a new AI system, based on a state-of-the-art algorithm called the YOLACT model [4], that integrates multiple endoscopic imaging modalities to detect and delineate the margins of early ESCC in real time.
Lost in the tunnel: Submucosal tunneling endoscopic resection guided by endoscopic ultrasound coils
Authors: Rodrigo Duarte-Chavez, Khaled Elfert, Michel Kahaleh
Journal: Endoscopy (2022)

Submucosal tunneling endoscopic resection (STER) is a technique that involves the creation of a tunnel to reach a lesion. The tunnel allows resection of lesions involving the muscularis and/or serosa, decreasing the risk of infection and/or fistula [1].
Simulation training of laparoscopic pancreaticojejunostomy and stepwise training program on a 3D-printed model
Authors: Jin Yang, Peng Luo, Zhifei Wang, Jiliang Shen
Journal: International Journal of Surgery (2022)

Laparoscopic pancreaticojejunostomy is among the most difficult and high-risk operations. Surgeons with low or moderate seniority rarely are allowed to perform this surgery in clinics. Therefore, there is an urgent need to develop a reliable simulation training model focused on laparoscopic pancreaticojejunostomy and an effective stepwise training program.Surgeons with different working experiences or exposure to different training programs at Sir Run Run Shaw Hospital were divided into four groups. Each was required to perform laparoscopic pancreaticojejunostomy using a designed three-dimensional dry lab model. All surgeons' baseline characteristics and surgical performance, including operation time and score, were recorded and analysed. The authenticity of the model was evaluated by four senior surgeons.The surgeon group with higher seniority had an older average age, longer working time, and had completed more laparoscopic cholecystectomy and laparoscopic common bile duct exploration procedures. Meanwhile, the surgeon group with higher seniority presented better operation performance, including shorter operation time and higher operation score in their initial simulation training. Resident surgeons who underwent stepwise training with the laparoscopic biliary-enteric anastomosis training program showed better initial performance than resident surgeons who underwent stepwise training with the laparoscopic basic suture training program. After repeated training, the surgeons showed improved surgical performance.Our pancreaticojejunostomy model showed a good degree of discernibility, as surgeons with more experience performed better with the model for their initial simulation training in laparoscopic pancreaticojejunostomy. Stepwise training of the laparoscopic biliary-enteric anastomosis training program helped surgeons obtain a better initial performance, and repeated simulation training on this model improved the surgeon's operative performance.
Endoscopic submucosal dissection in the colon with adaptive traction device: resection strategy and device setup
Authors: Mathieu Pioche, Louis-Jean Masgnaux, Jérôme Rivory, Thierry Ponchon, Timothée Wallenhorst, Romain Legros, Jérémie Jacques
Journal: Endoscopy (2022)

Endoscopic submucosal dissection (ESD) remains technically demanding. Traction seems to ease this procedure [1], but all traction strategies have their limitations [2], the main one being that traction force tends to decline as the dissection advances. An adaptive traction device, able to be tightened to increase traction during the procedure, has been described to overcome this limitation [3], but its installation remains challenging. We describe here the setup and strategy ([Video 1]) using the traction device (A-TRACT-2 + 2; Hospices civils de Lyon, France) combining two linked loops that could be tightened with two free loops to obtain a multipolar traction on the four edges of the lesion ([Fig. 1]).